1. Overfishing, pollution, coastal development and climate change threaten marine biodiversity globally and compromise the services that marine ecosystems provide. Systematic conservation planning (SCP) provides a framework to identify areas where actions can be effective in addressing these threats, while minimizing the costs of interventions. This study investigated the application of SCP in the Gulf of California, a marine hotspot where seven prioritization exercises have been undertaken. 2. The review of planning exercises showed that the use of SCP methods has progressed slowly (gaps include planning for land-sea connections and ecosystem services) and highlighted benefits and difficulties of applying SCP principles and tools. 3. Despite some convergence, important spatial differences were found in priorities between plans. Convergence was evident in well-studied shallow and benthic marine ecosystems. There were also important differences related to the planning approach, methods and extent. Divergence between methodological and spatial similarities between plans suggests that additional factors (e.g. manually delineating priority areas, incorporating updated datasets, random error), in addition to data and objectives, play an important role in defining the distribution of conservation priorities. 4. According to expert opinion, the implementation of new marine protected areas (MPAs) in the region has been influenced by some of the planning exercises. However, uptake of planning outputs has progressed slowly for many reasons (e.g. conflicting mandates and interests between organizations, limited technical capacities and resources, insufficient political commitment). Other benefits of planning included: developing institutional skills and knowledge; improving collaboration and coordination between organizations (including agencies, and local, regional and national NGOs); converging on the need to assess priorities for marine conservation in regional context; and building trust among organizations. 5. The existence of multiple marine conservation plans in the Gulf of California also highlighted some of the complexities and benefits of having multiple sets of priorities.>Copyright (c) 2013 John Wiley & Sons, Ltd.